TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Interpreting genetic variants from next-generation sequencing (NGS) data, including targeted resequencing and whole exome sequencing, presents a significant challenge.
• Efficient tools are needed to navigate, annotate, and visualize these variants to understand their functional implications.

Purpose of the Study:

• To introduce the Targeted RE-sequencing Annotation Tool (TREAT), a software designed for the facile navigation and mining of genetic variants.
• To provide integrated annotations and visualizations for variants, variant-hosting genes, and host-gene pathways.

Main Methods:

• TREAT integrates publicly available and in-house developed annotation datasets.
• It offers visualization capabilities for variants, genes, and pathways.
• The tool can be utilized as a stand-alone package or as part of a comprehensive workflow including sequencing alignment and variant calling.

Main Results:

• TREAT facilitates the exploration of variants identified through targeted resequencing and whole exome sequencing.
• The tool provides a rich set of annotations and visualizations, enhancing the interpretation of genetic variations.
• It supports the analysis of variants within the context of host genes and their associated pathways.

Conclusions:

• TREAT offers a valuable resource for researchers analyzing genetic variants from various sequencing approaches.
• The integration of annotations and visualizations streamlines the process of variant interpretation.
• The tool is freely available for non-commercial use, promoting wider accessibility in genomic research.